The Chosen
by Poohbear-29
Summary: Atlantis has been in their new home for a while now, but are they alone on the planet?
1. Chapter 1

Title- The Chosen

Rating-T

Author-Winnie

Disclaimer-I don't own SGA, but I enjoy keeping the characters alive at least in fanfiction.

Comments-This was supposed to be part of the virtual season, but can be read on its own.

Colonel John Sheppard sat alone on the highest terrace overlooking the city that was now his home. He could smell the ocean and sometimes, when the waves were particularly high, he could feel the salty mist on his skin. He loved coming here late at night while most people were sleeping and tonight was a particularly beautiful one. The sky was filled with a myriad of twinkling lights that sparkled off the water and seemed to dance off the wet surfaces of the lower structures.

Since returning from Earth, John would often find himself here, listening to the night sounds as the water lapped at the base of the city. John continued to watch the sky and smiled when a single star seemed to leave a fiery trail in its wake before disappearing below the horizon. This was happening with more and more frequency, but the scientists had told them it was simply part of the planet's pattern as it rotated on its axis.

Sheppard turned a complete circle when a strange sound reached his ears and frowned Yet, there seemed to be nothing out of the ordinary. The sound continued to grow, and it was starting to be uncomfortable. He tapped the radio, but couldn't say anything. He dropped to his knees as the sound increased rapidly and darkness clouded his mind. He covered his ears, but it did nothing to lesson the severity of the pain that now seemed to be embedded in his skull.

John knew he had to find out what was happening, and whether someone was attacking Atlantis, but his body suddenly seemed mired in sludge and it took every ounce of strength he had just to move an inch. He cried out and pulled the radio from his ear, but the sound didn't stop. If anything, it seemed to reach a pitch so high, it could shatter his ear drums.

'_Come to me, John…come be with me…I am waiting, John…'_

Sheppard cried out as the words inside his head increased in tempo, escalating into a screech that robbed him of the ability to breathe. He reached for the door's sensor, hoping and praying whatever this was did not involve Atlantis, but he was unable to think past the pain. To make matters worse, the door would not open for him.

His lungs felt like they were filling with liquid and John knew he was drowning, yet he was far from the ocean. He turned onto his back and stared up at the sky, panting with the effort it took to breathe.

'_Come to me, John…come be with me…I am waiting, John…'_

"Who…are you?"

'_I am the keeper of the deep, John, and you belong to me…I am waiting, John…' _

Darkness beckoned to him, and John Sheppard could no longer fight it. His body felt leaden, and he thought he heard voices, but couldn't be sure until someone knelt beside him and the deafening sound stopped. The silence left him gasping for air as a familiar figure finally came into focus. John tried to speak, but it was as if his vocal cords were gone because no sound escaped his throat.

"Easy, Sheppard, Beckett's on the way," Ronon Dex said worriedly. He'd been unable to sleep and decided to take one of his runs through the empty corridors of the city.

"Ronon, what happened?" Beckett asked as soon as the doors opened and he helped push the stretcher out onto the terrace.

"I don't know. I found him like this," Dex explained and moved back as the CMO and two nurses began an examination of the downed man.

"Colonel, can you tell me what happened?" Beckett asked.

Sheppard tried to speak, but nothing escaped as the shrill sound pounded his senses again, and threatened to send him into the darkness wavering on the edge of his awareness. He tried to shake off the nausea and dizziness as Beckett and his staff examined him and was suddenly aware that the noise that had incapacitated him seemed to have disappeared once more without warning.

"Colonel, we're going to get you on the gurney…"

"I'm okay, Doc," Sheppard said and sat forward with a sheepish grin as Beckett placed a restraining hand on his arm.

"Let me be the judge of that, Lad," Atlantis' CMO ordered. "Can you tell me what happened?"

"Didn't you hear it?" the colonel asked.

"Hear what?" Ronon asked.

"The noise, it was worse than fingernails on a chalkboard…"

"A what?" Dex asked.

"A chalkboard…I'll explain later," Sheppard said and tried to stand, but Beckett was not ready to release him.

"Come on, Colonel," the physician ordered and motioned to the gurney.

"I can walk, Doc," Sheppard said and stood up.

"All right, but we're going straight to the Infirmary. So you heard a noise…is that what knocked you on your backside?" Beckett said and smiled when Ronon chuckled softly.

"Real funny, Doc," the colonel said as they walked toward the transport area.

SGASGASGASGASGA

John knew the physician was only doing his job, but he'd quickly grown tired of the scans and was relieved when Beckett told him he was free to go. He headed toward his quarters, but only after promising Beckett he'd return to the Infirmary if it happened again.

John entered his room and looked at his bed as exhaustion suddenly caught up to him. He crossed the short distance and lay down without removing his clothing. It wasn't long before he slept, unaware of the siren call that beckoned to him. He stood up and made his way to the door, eyes straight ahead, yet unseeing as he stepped into the hallway.

The corridor was deserted with the lights turned down, but John knew his way around Atlantis. He nodded to several people as he passed, but did not speak. He knew this was wrong, but there was no denying the incessant voice inside his head.

'_Come to me, John…come be with me…I am waiting.' _

The voice was soft and lilting, as if an ethereal strand connected with his mind, beckoning for him to follow and John followed as if bewitched. His eyes remained open, but he moved as if sleep walking, yet he spoke to those who were unlucky enough to be up at the early hour.

'_Come to me, John…come be with me…I am waiting.' _

John tried to resist the call, but the words and the tone compelled him to do as the voice wanted. He walked along familiar corridors until he reached an area of Atlantis yet to be thoroughly explored and frowned when his hands reached out to touch the wall and a small panel appeared to his right. His right hand seemed to move of its own volition and he pressed a series of symbols and numbers and stood back expectantly.

'_You must not be discovered, John…come be with me…I am waiting.'_

"Excuse me, what are you doing here?"

John jumped at the sound of the voice so close to him and turned to find a young woman standing behind him. He recognized her as one of the new people from the science lab and that McKay had taken an interest in her because of her IQ and other attributes. He smiled as her mouth dropped open and he knew she had recognized him.

"I'm sorry, Colonel, I didn't know it was you."

"That's okay, Dr. Leonard, I couldn't sleep so I figured I'd take a look around before you and Dr. McKay explore the area tomorrow," Sheppard told her.

"Dr. McKay asked me to check out the first lab, but I got so wrapped up in the preliminaries I totally forgot. I was in bed before I even realized my mistake," Sylvie Leonard explained.

"Go on back to bed…I'm sure McKay will understand."

"Are we talking about the same man, Colonel?" Leonard asked and placed her hand over her mouth when she remembered who she was addressing. "I'm sorry…please don't report…"

'_Get rid of her, John…I am waiting…'_

"I won't report you, Dr. Leonard," Sheppard said.

"Thank you, Colonel."

"You're welcome…now go get some sleep or you'll be in no shape to face McKay in the morning."

"What about you, Sir, shouldn't you get some rest?"

"I will, as soon as I finish my run," Sheppard said with a smile and the woman seemed to realize she had overstepped her bounds. He watched her leave and dropped to his knees as the debilitating noise returned. His hands went to his ears and he gasped, but there seemed to be no way of stopping whatever this was until an ethereal figure stood over him.

'_You are of the chosen, John Sheppard, and must join me…I am waiting…' _

"Who…who are you?"

'_I am the keeper of the deep and you must join me.'_

"How?"

"_Go to the lowest level and follow the corridor. At the end you will find a chamber and inside there is a ship that is capable of traveling to the deepest part of the ocean. It is there that you will meet your true destiny. We will be waiting…I will be waiting…" _

John felt the pain ease and he fought to breathe past the nausea churning through his gut. He crawled to the wall and used it to help him stand as the world around him seemed to shift in and out of focus. A hand on his shoulder made him jump and he turned to find Teyla Emmagan watching him worriedly.

"John, is something wrong?" Teyla asked.

"No, I'm fine…just tired," Sheppard lied.

"You look very pale. Perhaps you should see Carson."

"Carson's probably sleeping. What are you doing up so late?"

"I was helping Kate in the botanical gardens. She's managed to make something she calls a hybrid and was trying to explain it to me."

'_Get rid of her, John…I am waiting and have very little patience…' _

"Who was that?" Teyla asked, confusion evident in her voice.

"Who was what?" Sheppard asked.

"I thought I heard someone speaking, but the voice was strange as if it came from inside my head," Teyla said, holding her fingers to her temples in bewilderment and looked around.

"I didn't hear anything," John lied.

'_She must not interfere…'_

"She won't," Sheppard said and saw the frown on Teyla's face.

"What's going on, John?"

"Teyla, just go."

"John, whoever that is…"

"It's no one, Teyla."

'_She must not be allowed to interfere, John Sheppard…'_

"Interfere in what?" Emmagan snapped.

'_You must come now, John, kill her now!'_

"No!" Sheppard said as the noise returned and he watched Teyla drop to her knees.

"John, what is that?" Teyla managed.

"Leave her alone and I'll come to you!" Sheppard said.

"John?"

"Please, Teyla, just stay where you are!"

'_She must not be allowed to stop you, John!' _

"Stop him from doing what?" Teyla asked, moaning as she sank to the floor, her eyes rolling back in her head.

"Leave her alone!" Sheppard said as Teyla writhed on the floor as if in excruciating pain.

'_She will be fine if you come to us now, John Sheppard.' _

John took a deep breath and knew there was no choice as Teyla's body twisted in a macabre dance that defied description. He turned toward the nearby transport and hurried inside. His last sight of Teyla told him whatever attack had been launched at her had stopped and he prayed she would be all right until help arrived.

John touched the pad that would enable the transporter to send him to the lowest level of Atlantis and took a deep breath before exiting onto the narrow platform overlooking a deep well that had filled with sea water and helped keep the base level. He knew there were several unexplored regions below the waterline and moved to the metal staircase leading to the lower floor.

'_Follow the corridor…it will take you deeper into the labyrinth beneath your city. There is a second tier that will take you through a tunnel as yet unexplored by your people. Once there, you will find what you need to bring you to us…to your destiny, John Sheppard.'_

Sheppard tried to ignore the voice, but it was no use as each time the pain returned, worse than before and he knew there was no choice, but to obey. He made it down the stairs and followed the corridor, holding his breath as the dank smell of decay reached his nostrils. His stomach churned, but he fought the nausea as he continued on his journey toward the unknown.

John lost track of time as he continued on a downward slope, fighting to stay on his feet as the floor turned treacherous with silt and debris. It felt like he'd left Atlantis behind and entered a dark region that had nothing to do with the splendor of the Ancient city he now called home.

Sludge, thick and noxious, slid down the walls and pooled on the floor around his feet, but John could no longer fight whoever was beckoning him forward. He reached for the wall, but his hand slipped in the mire that continued to ooze from the wall, though he managed to stay on his feet. The stench left him gasping for air and his eyes burned as he walked deeper into the bowels of Atlantis.

TBC


	2. Chapter 2

Ronon frowned as he leaned against the railing and knew something was wrong. Sheppard was usually here before he was, but this morning there was no sign of the other man. He walked along the upper corridor and headed for his friend's quarters and hoped Sheppard had simply slept in. He rounded a bend and nearly collided with Rodney McKay whose head was down as he studied something on the laptop he carried.

"Ronon, have you seen Teyla this morning?" the Canadian asked worriedly.

"No, haven't seen her since she knocked you on your ass yesterday," the Satedan said with a hint of a smile.

"She didn't knock me on my ass…I simply lost my balance after…"

"After she hit you," Ronon finished.

"I…what are you doing here anyway?" McKay asked in an effort to change the subject.

"Sheppard was supposed to meet me here," Dex answered. "Did you see him?"

"No," the scientist said with a frown. "Come to think of it, he wasn't at breakfast…you don't think he and Teyla are…no, couldn't be."

"What?"

"Perhaps they've finally realized there's a certain spark between them," McKay said.

"Sheppard don't seem like the type," Ronon said.

"True, he's more the love 'em and leave 'em cowboy type," the scientist said. "Well, I guess I should check her quarters."

"I was just headed for…"

An alarm sounded and both men hurried toward the main communication section where Woolsey joined them.

"What's happening?" McKay asked.

"We're not sure, but there are problems citywide," Chuck answered.

"What kind of problems?" McKay asked and moved to the main console, cursing when he looked at the readings. "When did this start?"

"There were a few glitches during the night, but they were easily fixed, but this is widespread and nothing we've done has come close to correcting the problems," Chuck told them.

"Has anyone heard from Colonel Sheppard or Teyla?" Woolsey asked, worried that both seemed to be missing.

"Sheppard was supposed to meet me for our morning run, but he never showed," Ronon explained.

"Teyla's unaccounted for as well," McKay said. "I'm running a citywide search for their transmitters now."

"Anything?" Woolsey asked.

"Give me a minute!" McKay snapped. "I've got Teyla, but she's not responding to my calls."

"Send a security team to her position and have Dr. Beckett informed of the problem," Woolsey ordered.

"I'm gonna check on Teyla," Ronon told them and hurried in the direction McKay gave him.

"I'm not getting a reading on Sheppard," McKay said softly.

"What do you mean?" Woolsey asked.

"I mean I'm not getting a reading. His subdural-transmitter should give us his location, but according to this, he's not even on the base," McKay answered. "Chuck, widen the search parameters to include the ocean floor."

"Nothing," Chuck told him after a moment.

"Could he have taken a Jumper and gone to check the mainland?" Woolsey asked.

"Not without us knowing and it looks like all Jumpers are present and accounted for. Chuck, was there any unauthorized use of the Stargate during the night?" McKay asked.

"No, Major Lorne's team was the only one to use it and they returned around midnight," Chuck answered.

"Dr. McKay, will you be able to correct the problems with Atlantis' operations?" Woolsey asked.

"Maybe, but I'll need Zelenka and several others to do a system-by-system analysis," McKay explained, silently cursing the problems he was seeing while adrenalin pumped through his veins.

**SGASGASGASGASGA **

For John Sheppard, Atlantis no longer existed, at least not the Atlantis he knew. In place of his beautiful inner city, he found debris-cluttered floors, and sludge dripping from walls that were crumbling from decay. The lights were dim and crusted with layers of silt that smelled strongly of death.

John fought the voice that continued to beckon him forward, but there seemed to be no way of taking back control as his feet slipped in the accumulated clutter of millennia of mistreatment. He managed to stay on his feet, eyes staring straight ahead in spite of his mind wanting to look around. The cloying stench of death permeated off the walls as he struggled deeper into the tunnel, and John wondered if somehow he'd triggered a hidden transporter and been sent somewhere far away from Atlantis.

The walls were diseased with an organism he'd never seen before. It was green, not unlike plants on earth, but these glowed with a light that burned his eyes. The plant's misshapen razor-like tendrils undulated, as if sensing his approach. He felt pain in his right calf as one of the tendrils cut through his skin, but didn't acknowledge it as the melodious voice returned.

'_Come to me, John Sheppard…come be with us…we are of the chosen and you belong with us.'_

John couldn't fight the urgency of the words as he exited the narrow corridor into a shimmering pool of translucent material. The substance covered a ship that only slightly resembled a Puddle Jumper. This one looked as if it had been lost here several millennia ago and he briefly wondered if it would ever fly again.

'_It will fly, John, but only when you wish it to…you must bring it to us and help us return to the place of our origin.' _

'_I'd rather not,'_ Sheppard thought, but moved toward the material as if his body was a controlled marionette and his will was no longer his own. It was hard, so hard that it felt like forever before his feet sank into the material and he moved away from solid ground. He could hear a whisper soft movement, as if butterflies were taking flight, but there seemed to be nothing near him that could make such a sound.

**SGASGASGASGASGA **

Ronon reached Teyla's location ahead of the security team and knelt beside the unconscious woman as the security and medical personnel arrived on the scene.

"Ronon, you'll have to move," Beckett ordered and moved to check the Athosian. He touched his fingers against her neck, relieved to find a strong, steady pulse. He could hear Ronon and the others talking, but his priority right now was Teyla Emmagan. The woman was unconscious, but there seemed to be no explanation to the naked eye.

"Doc, is she gonna be all right?"

"I don't know, Ronon. Right now we need to get her to the Infirmary and run some tests," Beckett answered as a nurse set up an IV before they loaded her onto a stretcher.

Ronon stood back and watched as Beckett's team hurried past him. The security team went with them, leaving Ronon standing alone in the corridor. He walked along the corridor, searching for any sign of John Sheppard, but there seemed to be nothing out of place. Instinct told him that the missing man was in trouble, but right now he had no way of knowing where to concentrate a search. He turned back just as Teyla was pushed down the corridor toward the nearest transport.

**SGASGASGASGASGA **

There was nothing of the real Atlantis around John anymore. Gone were the scents and sounds he associated with the beautiful city created by the Ancients. In its place was something out of his worst nightmares and John fought against it with every ounce of strength he had left, but it wasn't enough. The voice was back and continued to propel him forward in spite of the danger he felt. It reminded him of the Wraith queen who had forced him to his knees and tried to use her mind to control him. He shuddered uncontrollably as his right hand touched the ship and it came to life beneath his fingertips.

The ship seemed to shimmer, as if the translucent material it was partially submerged in was somehow responsible for its manifestation. John heard a metallic whine, as if clogged gears and hinges were coming to life. He moved along the edge of the craft and found a hatch that was barely above the thick line of sludge that held it above the surface. He stepped inside. The lights flickered and came to life, as if touched by unseen hands.

'_You will take the ship and join us, John.'_

'I don't know how to fly this ship.'

'_It will fly for you, John. It was built for your kind and has been waiting for you to come to us.'_

'I'd rather not.'

'_It is your destiny, John, there is no fighting what must happen. You will bring the ship to us and we will return to our place of origin."_

'Tell me who you are.'

'_You will find out when you join us, John. Take your place in the proper seat and you will find your true calling.'_

'If I refuse?'

'_You cannot refuse, John.'_

'Wanna bet?'

'_I do not understand the word bet, John, but I do understand pain.'_

John cried out when needle-like pain stabbed at his closed eyes. It roared through his skull while a keening wail echoed through the small craft. He grabbed his head as nausea churned through his gut, and fought to bring air into lungs that felt ready to collapse.

'_Do you understand pain, John?'_

'Stop!'

'_Will you do as you are told or should I turn the energy loose on your friends?'_

'No…leave them alone!'

'_Take your seat, John.'_

John used his left hand as a guide and supported himself against the wall as he moved through the debris that was scattered across the floor. He reached the pilot seat and sat down, breathing through tightly clenched teeth until the pain and nausea eased. He closed his eyes and thought about Teyla, silently praying that she was all right even as the engines fired up.

Unlike the Puddle Jumpers, this ship was more difficult to fly without inertial dampeners. The material it had been mired in seemed reluctant to release its prize, and John concentrated on just getting the ship up and out of the gooey substance. The craft's vibrations grew worse until John was sure it would break apart, but at the last minute, it pulled free, though it quivered before finally righting itself and hovering above the translucent matter beneath it.

'_Well done, John, now you must come to us. To me.' _

'Just how do I do that?'

'_I will guide you.'_

"I was afraid you were going to say that," Sheppard said, shocked that he'd actually voiced his thoughts aloud. John took a deep breath and found it hard to keep his eyes open. It felt like the ship was draining energy from him. There was pain, too, but it seemed inconsequential now that the craft flew on a preprogrammed course.

TBC


	3. Chapter 3

Rodney McKay had never been a patient man. Right now, he was finding it hard not to let his temper override his rapidly waning patience. Woolsey had been on his case since Sheppard's disappearance, but Rodney had no new information to give him. It looked like John Sheppard had simply disappeared and they had no way of finding out where he was or what happened to him.

Radek Zelenka and several other expedition members had been assigned the daunting task of working with him. Rodney had already lost his temper on several occasions since Teyla had been taken to the infirmary nearly four hours ago. Zelenka was smart, hell, if Rodney was truthful with himself, he'd rate Radek on a level that equaled his own, but McKay would never admit that to anyone.

"Rodney, have you run a diagnostic on the life support systems?" Zelenka asked.

"Not yet, I'm still working on the problems with the electrical system," McKay answered.

"We're also experiencing difficulty in dialing out," Zelenka told him.

"What the hell's going on? Did some moron decide to feed the gremlins after midnight?" the Canadian snapped.

"Gremlins?" Zelenka asked.

"Cute little creatures that turn deadly if fed after midnight. Right, McKay?" Ronon answered upon joining the group.

"Yes, but how did you know that?" the scientist asked and shook his head in disgust. "Oh, yeah, I forgot that was one of the movies Sheppard brought back on his last trip home."

"Rodney, there seems to be a power drain," Zelenka said and sat back when the console's lights dimmed and went out.

"What the hell did you do?"

"It wasn't me," Zelenka answered and held up his hands.

"Dr. McKay, power levels are dropping all over the city. Do you know what's causing it?"

"Unlike Colonel Sheppard, I'm not in tune with the city's inner workings," McKay said and snapped his fingers. "Wait a minute…Radek, run a check on the systems to see if there's any correlation to the 'Gremlin' attack and Sheppard's disappearance."

"Do you really think that's possible?" Ronon asked.

"A few years ago, I had no idea that gate travel even existed, let alone that I could live in another galaxy so a Sheppard-stealing Gremlin doesn't seem farfetched. Remember Sheppard happens to carry a very strong version of the ATA gene. He could somehow be connected with this city," McKay said, removing the cover from the console he'd been working at. "How's Teyla?"

"She's still out," Ronon answered simply.

"Does Carson know what's wrong with her?" McKay asked while disconnecting several wires.

"No, he's running tests," Ronon told him.

Rodney grunted and kept working. What was there to be said? They had missing people and an injured teammate. They had to find answers soon.

**SGASGASGASGA **

Carson Beckett checked the monitors next to Teyla's bed and was relieved to see the numbers were within the norm. They'd run every test he could think of, but nothing told him what had happened to the Athosian.

"Carson, did you see this?" Jennifer Keller asked and handed the physician a device that held the results of Teyla's latest tests.

"Are these numbers right?" Beckett asked worriedly.

"I double-checked them myself. Whatever happened to Teyla seems to be centered in her inner ear," Keller answered.

"She's going to have one hell of a headache when she wakes up and problems with balance too," Atlantis' CMO observed.

"Carson, it would take something drastic to cause this much damage," Keller said.

"Have you checked whether there's been any kind of explosion or concussion that could account for the damage?" Beckett asked and moved to check Teyla's ears.

"I checked with Rodney and he said he didn't think so, but with everything going on, it might not have showed up. I wonder if anyone else was affected."

"Surely they would have come to us if they were having problems," Beckett said and then frowned.

"What's wrong, Carson?"

"Teyla has a certain ability that could make her susceptible to this type of injury. She can sense the Wraith and we know very little about how that works...I wonder if she sensed something or heard something that caused this," Beckett said and looked at the readings once more. "I want to run another scan and see if we missed anything."

Keller nodded and moved to help set up the equipment. She was worried about Teyla, and hoped the woman would be all right. The fact that John Sheppard was missing also worried her, but for now they had to concentrate on the patient they already had.

**SGASGASGASGASGA **

John felt himself weakening as the tiny craft entered the murky depths of an ocean as yet unexplored. Through the window, he could see nothing but a darkness that seemed devoid of any living creatures. There was no sense of life surrounding him - nothing whatsoever, except the cloying atmosphere of a depth so deep it defied description.

John blinked and breathed through clenched teeth as the pressure seemed to build inside his skull. He wasn't sure whether it was the voice in his skull or the underwater pressure that caused the pain, but he knew he couldn't take much more. He swiped at something on his upper lip, and wasn't surprised to find blood on his fingers. He looked around for something to stop the flow, but there was nothing nearby and he simply used what was available. He tilted his head back and used his fingers to squeeze the bridge of his nose.

'_You are at the beginning of your journey to us, John Sheppard.'_

'How much further is it? I'm bleeding here…'

'_You must stop the flow of blood!'_

'No kidding!' Sheppard said and stood up. He moved away from the pilot seat and cursed as the ship tilted at an awkward angle and nearly sent him into a corner that had been severely damaged at some point in the last millennia. He moved back to the pilot seat and wasn't surprised when the Jumper righted itself.

'_You must not leave the pilot seat, John Sheppard!'_

'I don't have much choice if I want to find something to stop this!' Sheppard looked around, but still found nothing he could use. He finally admitted defeat and pulled off his shirt, keeping his mouth shut as the blood continued to flow. He tore a strip from the shirt and pressed it against his nose, clenching his eyes tightly in an effort to ease the building pressure behind them. The intensity of the throbbing crescendo threatened to drive him to his knees, but he understood he had to stay in control or risk a free dive to an even deeper depth of the ocean. It would mean certain death if he dove too fast without giving his body a chance to adjust to the pressure.

John stayed in the seat and pressed the piece of shirt against his nose, relieved when the bleeding finally stopped. He suddenly found it hard to stay focused and wondered how much more he could take as it felt like his body was being drilled with tiny needles.

'_You will adjust, John Sheppard.'_

'Glad you th…think so,' Sheppard said and was surprised when he looked through the window and noticed luminescent creatures swimming in weird patterns around the Jumper. These things were as big as a full grown cat with antennas that stuck out from what he guessed was the head.

'_They will not hurt you, John Sheppard. They protect the deep and our sanctuary. Follow them to your destiny.'_

'I don't think so.'

'_You have no choice. Your coming has been foretold since the dawn of our existence and you must fulfill what you were chosen for.'_

'And just what was I chosen for?'

'_You were chosen to lead us back to the surface where we will take back what was stolen from us.'_

'Stolen by who?'

'_You will find out when you have finished your journey.'_

John closed his eyes and tried to control the tremors that shook his body. The deeper the Jumper went, the harder it would be for him to escape. The voice was silent now and the pressure in his head eased to the point where he could concentrate enough to think clearly. The problem was if he thought too much, the voice would know what he was planning on doing. The trick was going to be keeping her in the dark.

TBC


	4. Chapter 4

"Radek, are you sure these readings are right?" McKay asked impatiently and kept hitting the keys on his laptop as if they were his worst enemy.

"I ran the diagnostic four times at a different terminal each time, Rodney," Zelenka answered with infinite patience. "The readings are correct."

"Then there's something wrong with the terminals!" McKay observed.

"With all of them?" Radek snapped.

"What other explanation is there?"

"Dr. McKay, have you completed your system analysis?" Richard Woolsey asked as he joined the two men in the Canadian's lab.

"It depends on what system you're asking about," McKay answered sharply. "We've been running a diagnostic on every system affected and the more we check, the more problems we're finding, yet the computer says that everything is working perfectly."

The lights flickered and dimmed as several alarms sounded throughout the city. McKay sputtered and worked his fingers over the keyboards until the lights came back on and the alarms were silenced. "Radek, were you able to find out where the power drains started this time?"

"No, it is the same as the last one and the one before that. Whatever is doing this seems to be causing random malfunctions, yet they do not show up in the system analysis," Zelenka answered as several new readings appeared on the screen in front of him. "Uh-oh."

"No, don't say that…uh-oh isn't even a word," McKay snapped and studied the new readings.

"Dr. McKay, what's happening?" Woolsey asked.

"There's some kind of virus in the system, but it wasn't there a few minutes ago and it's not acting like any virus I've ever seen. Radek?"

"I agree, Rodney. I don't think it is a virus," Zelenka said. "It doesn't have…"

"It could be the Pegasus version of a virus, but where would it have come from?" McKay interrupted.

"There are several worlds that have advanced to the point where they could cause a virus. The Genii comes to mind," Woolsey answered.

"The Genii are supposed to be allies," McKay said and then waved the others off before they could say anything. "I know they haven't done anything to solidify our friendship, but they wouldn't do anything this obvious or this stupid…would they?"

"They have done worse in the past," Chuck answered.

"Yes, but not since Ladon helped us find Sheppard," McKay reminded them.

"What about the Wraith? Could they have found a way to corrupt the system?" Zelenka suggested.

"Maybe, but the Ancients set up protocols that would immediately stop any Wraith attempt to infiltrate the network. Although, like everything else those protocols can malfunction if someone knows how to get around them" McKay told them as he thought about Michael and the Wraith Queen he'd brought to Atlantis on a mission to disperse the Wraith-transforming gas on enemy Wraith ships. Thankfully, that Wraith queen and her ship had been destroyed before she could use the information she'd collected.

"Dr. McKay, you mentioned this could all be due to Colonel Sheppard's disappearance. Have you discounted that possibility?" Woolsey asked.

"No, I still think that's the problem," McKay said. "Finding Sheppard just might be the key to fixing the problems.

"Is there any way to test that theory?" Woolsey asked.

"No, there isn't a program we can run to see if Sheppard and the city are actually in tune with one another!" McKay snapped impatiently. "Look, we need to figure what's going to be affected before the whole system crashes."

"If this is related to Colonel Sheppard's ATA gene, then why is it none of the other ATA carriers affected the city in this way before, Dr. McKay?" Woolsey asked.

"Colonel Sheppard is the strongest natural ATA carrier in Atlantis," McKay answered. "It's weird, but from the beginning, the city reacted to his presence. Don't get me wrong because others with the ATA gene, whether natural or due to Carson's gene therapy, can affect the city wide systems and run the programs, but no one has ever seemed to do it with such ease. It is the reason Elizabeth wanted him on this expedition."

The lights flickered again, but there were no alarms this time. However several other systems shut down completely and couldn't be restarted for several minutes. McKay and Zelenka worked together with several other techs, but there seemed to be no answer to the dilemma.

**SGASGASGASGASGA **

Major Evan Lorne led the search party through several of the lower levels, but so far they'd come up empty. They were working under the assumption that Teyla Emmagan and John Sheppard had been together when she was injured. It was a weak assumption, but it was the only one they had and Woolsey wanted it pursued.There were several places they needed to search, but Lorne suspected they wouldn't find the missing colonel, not when there was no sign of him in the city.

There were a variety of teams searching the upper levels, but they'd also come up empty. To add to their dilemma, the citywide problems were making the search even harder. The lighting in this section was minimal at best, but since the power outages, they'd been forced to resort to flashlights. They'd already searched several otherwise unexplored labs, but found nothing that might give them a clue as to what happened to Teyla and Sheppard.

"Ronon, don't go too far ahead," Lorne ordered as the Satedan moved further along the darkened corridor.

"Major, I think we need to get McKay down here."

"What is it, Lieutenant?"

"I'm not sure, but there's a hologram here. Just like the one Dr. Beckett found when we first came to Atlantis. It just seems to be malfunctioning right now."

"What's new about that?" Lorne asked no one in particular as he clicked on the comm link.

"Did you find Colonel Sheppard, Major?" Woolsey asked hopefully.

"No, Sir, but Lieutenant Reid found a malfunctioning hologram…figured maybe Dr. McKay would want to take a look at it," Lorne told him.

"Dr. McKay is busy, but make sure you catalog it so he can check it out when he's completed his analysis of the city's programs," Woolsey told him.

"Yes, Sir…Lorne out," the major said as he turned back to the lieutenant. "Lock it down and get on with the search."

"Yes, Sir," Reid answered and moved away from the console and watched the image flicker before it faded away completely.

"Where'd Ronon go?" Lorne asked.

"Down the corridor…I thought I saw him go left," Reid answered. "Want me to go after him?"

"No, you keep checking the doors. I'll see what Ronon's found," Lorne answered and hurried down the corridor. He turned left and spotted the bigger man standing about halfway down the next hall. "Ronon, I thought you were waiting for the rest of us?"

"Figured you'd catch up," Dex told him and pointed toward the corridor that seemed to be an offshoot of the one they were standing in. "This wasn't here when I walked by, but I accidentally touched that panel and it opened up."

"What the hell's that god-awful smell?"

"Smells like something died down there," Dex answered and pointed to the footprints someone had made in the layer of dust and silt.

"Colonel Sheppard, it's Lorne, can you hear me?" Lorne called and repeated it over his comm link without success.

"I don't think he's down there," Ronon answered.

"Those are military issue boots and the only one I can think of who could have made them was Colonel Sheppard."

"I know, but if he was down there, he'd answer."

"Not if he's hurt or unconscious," Lorne said, wishing the lights would come back on. "We need to get down there."

"Give me your flashlight and I'll check it out," Dex said.

"Not alone you won't," Lorne said and tapped his comm link. "Lieutenant Reid, Ronon found another staircase leading down and we're going to check it out. If you don't hear from me in fifteen, get another team and find out if McKay can get the lights on down here."

"Yes, Sir," was Reid's quick reply.

Lorne shone the light down the stairwell and wrinkled his nose at the strong smell of death and decay that permeated off the walls and steps. "Maybe we should wait for backup."

"What if he's hurt?" Ronon said and began moving down the stairwell.

"Damn, just – just be careful…this stuff is slippery," the major explained and latched onto the railing, grimacing in distaste when his hands encountered a sticky residue. With each step he took, his nose burned with the cloying stench that seemed to grow stronger the further down they went.

Ronon didn't touch the rails, though he did wonder what or who had made the material that seemed to coat everything in a thick layer of slime. He counted each step and glanced back toward the upper level when they reached fifty steps. The walls seemed to be glowing and he glanced down as he spoke. "Shut off the flashlight for a minute."

"What? Why?" Lorne asked.

"Just do it," Dex said and waited for the other man to comply.

The darkness lasted less than ten seconds as the coating on the walls and stairs began to glow with a strange, eerie luminescence that reminded Lorne of something he'd seen in a horror movie.

"We need to get a science team down here and find out what this is," Lorne observed.

"Just warn them to wear nose plugs," Dex observed.

"How much further down do we go?" Lorne asked. He knew he could order Ronon back, but he found out long ago that Sheppard trusted the Satedan implicitly. They'd all learned to trust their instincts where the people of the Pegasus Galaxy were concerned and had made several allies, and even more enemies.

"Don't know," Ronon said and began to move deeper into the depths of Atlantis. They didn't need flashlights anymore, but he wished he had one of the masks they used when the air was un-breathable. He heard Lorne gagging behind him and wondered how much further they could go without being sick.

"Ro…Ronon, think we n…need to go back," Lorne told him. "If Colonel Sheppard is d…down here, he'll probably need a medical team. Th…there's no telling what we're bre…breathing, but my lungs are bur…burning."

Ronon knew the other man was right and reluctantly turned back and started up the stairs. It was hard to breathe and he leaned against the wall to catch his breath as Lorne finally caught up to him. They reached the top just as Reid and the others turned the corner and made their way toward them.

"We need…need," Lorne began, but couldn't quite get the words out as he sank to the floor.

"Better get Beck…Beckett," the Satedan told them and heard Reid calling for a medical team just before he blacked out.

TBC


	5. Chapter 5

'_You must come now, John, kill her now…She must not be allowed to stop you.'_

Teyla moaned softly and tried to open her eyes, but the pain refused to ease even as she struggled against the nightmare still haunting her. She could hear a voice, but could not make sense of what it was saying, but it sounded insistent. She fought her way out of the dreams and away from the strange, compelling voice that continued to echo inside her head.

"That's it, Teyla, come on now and open your eyes, Lassie."

"Carson, there's an emergency on one of the lower levels. I'm taking a team down there," Keller said.

"Is it Colonel Sheppard?" Carson asked, glancing at Jennifer as she prepared to leave.

"I don't think so, but it's in the same area where Teyla was found," Keller said and then she hurried away.

"Carson," Teyla managed, her voice weak as she shifted on the bed.

"That's right, Lass, how do you feel?" Beckett asked.

"My head hurts," Teyla answered and tried to sit up.

"Easy now, just lie still," the physician ordered.

"What happened?"

"That's what we were hoping you could tell us," Beckett said with a slight smile as he checked her eyes.

"I…I was supposed to meet Rodney," Teyla said, frowning as she tried to make sense of her jumbled thoughts.

"Aye, Rodney told us you were supposed to meet him."

"I think I saw Colonel Sheppard," Teyla said and closed her eyes as she tried to grasp something that seemed just out of her reach. "There was someone else there. I heard a voice…a woman's voice."

"Did you recognize it?"

"No," Teyla answered.

"What did the voice say?" Beckett asked.

"I am not sure…something about John being chosen," Teyla said and moaned as the pain returned each time she tried to grasp the illusive memories. "I'm sorry. I can't remember."

"It's okay," the physician told her and placed a gentle hand on her shoulder. "You should rest now."

"I am tired," Teyla whispered and closed her eyes.

Carson looked at the monitors, relieved to find her readings had improved. He thought about Colonel Sheppard and what Teyla had said and hoped she could shed some more light on what had happened to him. He quickly updated her file and turned toward the main door as it opened and Keller's team returned.

"How is she, Carson?" Keller asked.

"She was awake and that's a good sign, but she didn't say much," Beckett answered. "What happened to these two?"

"Not sure, but it could be some kind of exposure to an unknown gas or toxin." Keller answered. "They found another staircase leading deeper into the base of the city and decided to explore it without checking it out first. I could use a hand here if you're free."

Beckett nodded and moved to the gurney holding Lorne as a nurse finished hooking up the monitors and he glanced at the readings. Although the oxygen intake was a little low, it was nothing dangerous and everything else seemed to be within the normal parameters. An alarm sounded as the lights flickered and blinked out only to come back at half the power of emergency lighting. Carson quickly checked Lorne's readings and pressed the button to begin a scan.

"Easy, Ronon, just be still while I check you out," Keller ordered.

"I'm okay, Doc, just got a little…"

"Too much gas or whatever is down there," Jennifer told him.

"Lorne okay?" Ronon asked and again tried to sit up.

"He's coming around," Beckett answered as the scan completed its trek up and down the major's body. "Easy now, Lad, just relax and let me get the results of the scan before you go trying to get up. Paula, I want blood tests run on both of them."

"Yes, Doctor," Paula Leland said and pulled a cart closer as Richard Woolsey entered the infirmary and strode toward them.

"How are they?" Woolsey asked. He found it awkward at times when speaking to the physician who was back in position as Atlantis' CMO.

"They seem to be okay, but I want to run several more tests before we release them," Beckett answered. "Has there been any word on what's causing the problems with the city?"

"Dr. McKay has teams all over the city, but so far everything still points to an association with Colonel Sheppard's disappearance," Woolsey said and turned to Lorne as the nurse finished taking blood samples.

"Mr. Woolsey, I think we may have found out where Colonel Sheppard went, but we need to get down there to check it out properly," Lorne explained and ignored Beckett's warning glare as he sat on the edge of the bed.

"Lieutenant Reid is getting a team together, but no one goes down there until we take some readings," Woolsey stated.

"Sheppard could be hurt," Dex said simply as the nurse took blood from his arm.

"We don't know that for sure. After what happened to you and Major Lorne, I'd rather not take the chance of anyone else getting hurt. Colonel Sheppard would be the first…"

"To go down there if it was one of us!" Dex stated and stood on shaky legs.

"That may be, but for now, we do this my way," Woolsey ordered. "Carson, I'll be in my office, so please let me know as soon as you have the test results."

"I will," Beckett said and looked at the two men. "Now, you two aren't going anywhere until I'm sure whatever you inhaled down there isn't going to cause any surprises that could land you in here for a week…Lord knows I doubt any of my staff could handle it."

**SGASGASGASGASGA **

John Sheppard had given up on trying to keep track of where he was going. The darkness outside the Jumper was broken only by the shimmering creatures that seemed to be guiding the ship deeper into the murky depths of the ocean. His nose had finally stopped bleeding, but the throbbing in his skull had gone from annoying to nauseatingly painful. The voice was quiet for now, but he had a sense that whoever was behind the voice was watching him.

John forced his eyes open and cried out as he tried to make sense of what he was seeing. The creatures outside his window had grown to twice the size of their shallower siblings and their eyes were filled with a sickeningly bright light. He remembered driving down a wooded street in the mountains with nothing but his car's headlights for company when a bright light appeared directly in front of him, temporarily blinding him. He'd barely managed to stop the car from going over the embankment, while the idiot in the other car had continued along the road without stopping.

'_John, you must not look directly into their eyes.'_

'Now she tells me,' Sheppard thought and frowned when he heard the unmistakable sound of laughter.

"_You did not ask, John Sheppard.' _

'Are we there yet?'

'_Are we where yet?'_

'Wherever the hell you're taking me.'

'_It will not be much longer before you reach your destination and your destiny. When the ship stops, you must wait for me to come for you.'_

'What happens if I don't?'

'_You will be unable to breathe the air down here and must not attempt to leave the ship. I will not allow you to ruin our chance to reach the surface and take back that which belongs to us. We are of the chosen and so are you.'_

'Chosen for what?'

'_That too will be revealed when the time is right. Close your eyes and rest. The light will be too bright for your eyes to adjust. We do not wish to blind you.'_

John did as he was told and found himself drifting toward sleep as the silence surrounded him once more. His thoughts kept returning to Teyla. He hoped someone had found her, because he did not want to be responsible for another death.

TBC


	6. Chapter 6

Rodney McKay had never felt so tired in his life, but he didn't have time to sleep. He glanced sideways at Zelenka who was passed out at the console. Nearly thirty hours had passed since Sheppard's disappearance and slowly, but surely every system had been affected. Some of it was simple, and they'd managed to get several programs back online, but if it continued, Atlantis could very well sink to the bottom of the ocean again. This time, there would be no stopping the water from flooding the city, because they had no way to regulate the program that controlled the shields with things as they were.

McKay thought about the Ancients and cursed them for making every single program reliant on the ATA gene carriers. He knew they'd done it because of the threat the Wraith represented, but they hadn't taken into account what would happen if they died out in the Pegasus Galaxy.

Zelenka's soft snores made McKay long for his own bed, but instead he reached for the cup of extra strong black coffee next to the laptop. He took a small sip, grimacing as it burned his tongue, but swallowed anyway with a soft curse that had Radek murmuring something unintelligible.

Rodney tapped on several keys, bringing up the schematics as he checked to see what they'd found out about the new, as yet unexplored, region of Atlantis. Ronon and Lorne had been released from the infirmary and were planning to lead a team down into the depths of what smelled like a cesspool. They'd taken readings of the air in the stairwell, but there was no way of identifying what the stench was. Nearest they could come, it was centuries, if not millennia of death and decay locked up until the hidden panel was opened, possibly by the missing colonel and later by Ronon.

Rodney heard the door open behind him and turned to see Richard Woolsey standing there. The man looked as tired as he was, but McKay didn't tell him that as Atlantis' leader came over to stand at his side.

"Have you found anything new?" Woolsey asked.

"Not really, although Radek did manage to isolate several lines of code that might help us find a way around the ATA gene issue. It would only be a quick fix, but at least we wouldn't have to put up with the power outages and disruptions to the programs," McKay explained.

"That is good news…isn't it?" Woolsey asked when McKay didn't seem all that enthused with the news he'd imparted.

"Yes, it is, but I keep thinking the Ancients left themselves in quite a mess because everything is so reliant on the ATA gene. I know why they did it and maybe it was the right choice at the time, but it's like the old analogy of putting all your eggs in one basket."

"Analogies are not always correct," Woolsey said. "Major Lorne and Ronon Dex are getting ready to check the lower level. Ronon seems to think that's where Colonel Sheppard went after meeting Teyla."

"How is Teyla? Have you seen her?"

"I spoke with Dr. Beckett and he said she was awake for a few minutes, but she didn't shed any light on what happened," Woolsey explained. "Dr. McKay, I've been thinking about the city and the problems we seem to be having."

"Join the club…I believe that's what's been on everyone's minds," McKay snapped tiredly as he studied the new readouts on the laptop. He glanced at Zelenka and added, "At least everyone who's still awake."

Woolsey ignored Rodney's comment. "If the city is reacting to Colonel Sheppard's disappearance…"

"Oh, believe me, it is. It's happened before," the Canadian said.

"It has?" Woolsey asked.

"Yes, several times, but never on this level. Usually, it's just the lights flickering or a transporter not working, but it's usually something easily traced back to Sheppard," McKay said. He frowned when he thought about the answer he'd just given Woolsey. "You know perhaps this isn't just about Sheppard. There could be outside influences at work here."

"Outside influences like the Genii?" Woolsey asked.

"Oh, please, get past the Genii. They may be technologically advanced for the Pegasus Galaxy, but I doubt they can infiltrate Atlantis' systems," McKay said.

"They did a pretty good job of taking over the city during a storm," Woolsey offered.

"True, but we were caught off guard and didn't know much about the city at that point. The same scenario can't happen now…not with the fail safes we have in place."

"Then who?"

"That's the question now, isn't it?" McKay said and tapped his finger on his chin before sitting up and opening several new windows on his laptop. "If there is an outside influence, then they must be capable of interacting with the Ancient technology that runs Atlantis. I may be able to create a program that will trace any unauthorized access to the city's systems. It might even help us find Sheppard."

"Let me know…"

"Yes, yes…busy genius at work," McKay snapped impatiently. "Radek, wake up for crying out loud! We have work to do!"

**SGASGASGASGASGA **

The ship glided through the shimmering light as the creatures undulated, sending translucent waves crashing against the damaged hull of the craft. Sheppard had no idea how long he'd been drifting through the deep ocean, but his body was weary and his leg tingled. He looked down and saw blood on his pants leg and briefly wondered where it came from. He tugged on the material and found it stuck to his leg and gritted his teeth as he pulled it away from the wound.

John lifted the leg of his pants and frowned when he saw the deep, jagged wound to his right calf. It was bleeding again, and he reached for another piece of his shirt. The wound stung, but it wasn't bad until he moved his right leg and tied the makeshift bandage around it.

'_Welcome, John Sheppard.'_

"Uh…what?" Sheppard said and realized the ship was no longer moving. He released his hold on the leg of his pants and stared out the window at a world that looked like something out of a post-apocalyptic movie. The walls were of the same organism that had invaded the lower level of Atlantis and he wondered just how these creatures had managed to invade the city.

'_You will find your answers soon, John Sheppard. Come, I am waiting for you.'_

'That's what I'm afraid of,' Sheppard thought and he heard soft laughter coming from outside the ship. He stood up, wincing as he put pressure on his right leg. He limped toward the back hatch and waited expectantly for it to open. He didn't have long to wait and caught scent of something that made his stomach churn.

"_Come, John Sheppard.'_

'I'm coming. You people really should clean up when you know company is coming…smells like something died in here.'

'_Many of my kind have died here, John Sheppard, but you will change that.'_

'I will? How?'

'_You will see. Come out of the ship…do not be afraid, John Sheppard, you will not be harmed.'_

John wanted nothing more than to stay in the ship, but felt compelled to move as the hatch finished opening. He stepped out onto the uneven platform, but then had to grab the side of the craft in an effort to stay on his feet. The air burned his lungs and he fought the urge to be sick as he stumbled forward, glancing around in an effort to familiarize himself with his surroundings.

The walls of the cavernous chamber seemed to be alive with the creatures he'd seen shadowing the puddle jumper, but there were slight differences in color and size. They lit up the area with an iridescent light that was too bright for his eyes and added to the blinding headache he'd felt when he left the puddle jumper behind. Pain swelled to a sickening crescendo as he pitched forward and landed on a surface that seemed to move even as consciousness left him.

TBC


End file.
